Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,871,650 G→C 8.7% L259V (CTG→GTG)  PP_3420 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,871,6500GC 8.7% 130.1 / 4.0 46L259V (CTG→GTG) PP_3420sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (21/21);  new base C (2/2);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

CTTCTGCGCAGCAGCGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCC  >  NC_002947/3871501‑3871792
                                                                                                                                                     |                                                                                                                                               
cttctGCGCAGCAGCGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAg                                                                                                                                                 <  1:595308/150‑1 (MQ=255)
         agcagcGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCat                                                                                                                                        >  2:18647/1‑150 (MQ=255)
         agcagcGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGACTGTcctgctgcacctgctgcag                                                                                                                                        <  2:447166/150‑2 (MQ=255)
              cGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATAtgtg                                                                                                                                   <  2:13798/150‑1 (MQ=255)
                       tttCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGgc                                                                                                                          >  1:428434/1‑150 (MQ=255)
                            tGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACg                                                                                                                    >  1:241253/1‑150 (MQ=255)
                                  aGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAg                                                                                                              <  1:246073/150‑1 (MQ=255)
                                      cGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACa                                                                                                          <  2:245721/150‑1 (MQ=255)
                                             ggAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGaa                                                                                                   <  2:53367/150‑1 (MQ=255)
                                                gCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATc                                                                                                                 <  2:630224/133‑1 (MQ=255)
                                                gCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATc                                                                                                                 >  1:630224/1‑133 (MQ=255)
                                                   tATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGAt                                                                                             <  1:654754/150‑1 (MQ=255)
                                                     tGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCa                                                                                           >  1:367803/1‑150 (MQ=255)
                                                     tGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCa                                                                                           <  1:18647/150‑1 (MQ=255)
                                                      gTTGGCCAGCGGGTTACGCATGCTGTGAGCCTCTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCaa                                                                                          >  2:491559/1‑150 (MQ=255)
                                                            cAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGcccc                                                                                    >  1:631942/1‑150 (MQ=255)
                                                                   ttACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCACCTgcagcaggac                                                                                                                                     >  1:396705/1‑91 (MQ=255)
                                                                   ttACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCACCTgcagcaggac                                                                                                                                     <  2:396705/95‑5 (MQ=255)
                                                                              gtgAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGc                                                                  >  2:775722/1‑150 (MQ=255)
                                                                                   ccACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGa                                                             >  2:734185/1‑150 (MQ=255)
                                                                                    cACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAg                                                                    <  1:551232/142‑1 (MQ=255)
                                                                                    cACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAg                                                                    >  2:551232/1‑142 (MQ=255)
                                                                                     aCTGCCGACTACATTTCACCCAGCGCAACGTCGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCTCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATc                                                           <  2:163149/150‑1 (MQ=255)
                                                                                      cTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCa                                                          >  2:3306/1‑150 (MQ=255)
                                                                                           gacgacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGca                                                       <  2:402699/148‑1 (MQ=255)
                                                                                           gacgacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGca                                                       >  1:402699/1‑148 (MQ=255)
                                                                                             agacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATa                                                   <  1:162805/149‑1 (MQ=255)
                                                                                                                  gTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGAt                              <  1:3306/150‑1 (MQ=255)
                                                                                                                    aGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTgccgc                                                                                                                               <  1:144515/52‑1 (MQ=255)
                                                                                                                    aGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTgccgc                                                                                                                               >  2:144515/1‑52 (MQ=255)
                                                                                                                       tttCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                         >  1:443724/1‑150 (MQ=255)
                                                                                                                            cTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAg                                                                    >  2:161471/1‑102 (MQ=255)
                                                                                                                            cTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAg                                                                    <  1:161471/102‑1 (MQ=255)
                                                                                                                                 caccaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTAGCGGCTc               >  1:515940/1‑150 (MQ=255)
                                                                                                                                  accaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTcc              <  1:734185/150‑1 (MQ=255)
                                                                                                                                  accaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTcc              <  1:491559/150‑1 (MQ=255)
                                                                                                                                    caGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCtt            <  2:367803/150‑1 (MQ=255)
                                                                                                                                      gCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGACCCAGAACAGGCCGAAGTAGATCAACCCCCCACCCCCCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGTTCTTGCGGCTCCTTGt          <  2:241253/150‑1 (MQ=255)
                                                                                                                                         tGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGa       >  1:555056/1‑150 (MQ=255)
                                                                                                                                           atatgctgcACCTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                         >  1:298031/4‑130 (MQ=255)
                                                                                                                                           atatgctgcACCTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                         <  2:298031/127‑1 (MQ=255)
                                                                                                                                             ctgctgCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTc   >  1:113204/1‑150 (MQ=255)
                                                                                                                                              tgctgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTcc  >  2:257737/1‑150 (MQ=255)
                                                                                                                                              tgctgcAGGTGCAGCATATGTGCCGCCCGGCCCGTAGAGATGGCTGATGCC‑ATGGAGATTAACGCCCCACCCCCCAGGGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTcc  <  1:775722/150‑1 (MQ=255)
                                                                                                                                                 tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGcaca                                                     <  1:769307/96‑1 (MQ=255)
                                                                                                                                                 tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGcaca                                                     >  2:769307/1‑96 (MQ=255)
                                                                                                                                                 tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAgg                          >  1:180963/1‑123 (MQ=255)
                                                                                                                                                 tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAgg                          <  2:180963/123‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                               
CTTCTGCGCAGCAGCGTTGGCGGTTTCCTGGGCAAGTTCGGCGCTGGAGCGTATGTTGGCCAGCGGGTTACGCATGCTGTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCC  >  NC_002947/3871501‑3871792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑